These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.
Usage
random_mic(size = NULL, mo = NULL, ab = NULL, ...)
random_disk(size = NULL, mo = NULL, ab = NULL, ...)
random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...)Arguments
- size
desired size of the returned vector. If used in a data.frame call or
dplyrverb, will get the current (group) size if left blank.- mo
any character that can be coerced to a valid microorganism code with
as.mo()- ab
any character that can be coerced to a valid antimicrobial agent code with
as.ab()- ...
ignored, only in place to allow future extensions
- prob_RSI
a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)
Details
The base R function sample() is used for generating values.
Generated values are based on the EUCAST 2022 guideline as implemented in the rsi_translation data set. To create specific generated values per bug or drug, set the mo and/or ab argument.
Examples
random_mic(25)
#> Class 'mic'
#> [1] 0.0625 64 >=256 32 32 128 0.01 32 2 32
#> [11] 0.002 >=256 128 0.5 0.5 128 1 0.25 16 64
#> [21] 16 0.125 8 64 0.01
random_disk(25)
#> Class 'disk'
#> [1] 7 49 39 44 46 6 28 50 31 38 13 26 49 49 16 23 22 43 44 26 45 38 46 50 41
random_rsi(25)
#> Class 'rsi'
#> [1] S S I S S S S I S R I I S I R S I I S S S I S R I
# \donttest{
# make the random generation more realistic by setting a bug and/or drug:
random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
#> Class 'mic'
#> [1] 4 0.025 0.25 0.5 8 0.5 2 0.025 1
#> [10] 0.002 <=0.001 0.0625 0.125 0.005 4 16 <=0.001 <=0.001
#> [19] 0.5 0.01 64 0.025 8 0.5 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=16 >=16 8 4 1 4 0.5 1 1 0.5 4 4 >=16 2 1
#> [16] 0.5 >=16 0.5 4 1 2 4 4 1 >=16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 1 1 <=0.125 1 0.25 >=16 1 <=0.125
#> [10] 4 <=0.125 >=16 8 8 0.25 8 0.25 2
#> [19] 0.5 <=0.125 0.25 2 0.25 4 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 46 29 40 23 36 28 16 26 47 44 26 47 47 42 47 47 13 25 47 42 43 38 44 50 31
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 16 17 11 16 15 16 13 15 15 12 13 17 16 11 12 13 11 14 13 12 16 12 17 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 26 15 16 18 21 20 23 24 19 20 20 27 24 16 24 19 19 18 16 25 24 22 21 22
# }